scholarly journals Characterizing the Leaf Transcriptome of Chrysanthemum rhombifolium (Ling et C. Shih), a Drought Resistant, Endemic Plant From China

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenjie Zhang ◽  
Hongyuan Xu ◽  
Xiaxia Duan ◽  
Jing Hu ◽  
Jingjing Li ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Defense Mechanism ◽  
Endemic Plant ◽  
Illumina Platform ◽  
Protein Database ◽  
The Public ◽  
Protein Databases ◽  
Kegg Pathways ◽  
Plant Resource ◽  
Leaf Transcriptome

Chrysanthemum rhombifolium (Ling et C. Shih), an endemic plant that is extremely well-adapted to harsh environments. However, little is known about its molecular biology of the plant's resistant traits against stress, or even its molecular biology of overall plant. To investigate the molecular biology of C. rhombifolium and mechanism of stress adaptation, we performed transcriptome sequencing of its leaves using an Illumina platform. A total of 130,891 unigenes were obtained, and 97,496 (~74.5%) unigenes were annotated in the public protein database. The similarity search indicated that 40,878 and 74,084 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Of these, 56,213 and 42,005 unigenes were assigned to the Gene Ontology (GO) database and Cluster of Orthologous Groups (COG), respectively, and 38,918 unigenes were mapped into five main categories, including 18 KEGG pathways. Metabolism was the largest category (23,128, 59.4%) among the main KEGG categories, suggesting active metabolic processes in C. rhombifolium. About 2,459 unigenes were annotated to have a role in defense mechanism or stress tolerance. Transcriptome analysis of C. rhombifolium revealed the presence of 12,925 microsatellites in 10,524 unigenes and mono, trip, and dinucleotides having higher polymorphism rates. The phylogenetic analysis based on GME gene among related species confirmed the reliability of the transcriptomic data. This work is the first genetic study of C. rhombifolium as a new plant resource of stress-tolerant genes. This large number of transcriptome sequences enabled us to comprehensively understand the basic genetics of C. rhombifolium and discover novel genes that will be helpful in the molecular improvement of chrysanthemums.

scholarly journals Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four Papaver Species

Data ◽  
2018 ◽  
Vol 3 (4) ◽  
pp. 55 ◽  
Author(s):  
Dowan Kim ◽  
Myunghee Jung ◽  
In Ha ◽  
Min Lee ◽  
Seok-Geun Lee ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Bioinformatics Analyses ◽  
Kegg Pathways ◽  
Benzylisoquinoline Alkaloid ◽  
Development Life Cycle ◽  
The Family ◽  
Leaf Transcriptome ◽  
Secondary Metabolite Biosynthesis

Poppies are well-known plants in the family Papaveraceae that are rich in alkaloids. This family contains 61 species, and in this study we sequenced the transcriptomes of four species’ (Papaver rhoeas, Papaver nudicaule, Papaver fauriei, and Papaver somniferum) leaves. These transcripts were systematically assessed for the expression of secondary metabolite biosynthesis (SMB) genes and cytochromes, and their expression profiles were assessed for use in bioinformatics analyses. This study contributed 265 Gb (13 libraries with three biological replicates) of leaf transcriptome data from three Papaver plant developmental stages. Sequenced transcripts were assembled into 815 Mb of contigs, including 226 Mb of full-length transcripts. The transcripts for 53 KEGG pathways, 55 cytochrome superfamilies, and benzylisoquinoline alkaloid biosynthesis (BIA) were identified and compared to four other alkaloid-rich genomes. Additionally, 22 different alkaloids and their relative expression profiles in three developmental stages of Papaver species were assessed by targeted metabolomics using LC-QTOF-MS/MS. Collectively, the results are given in co-occurrence heat-maps to help researchers obtain an overview of the transcripts and their differential expression in the Papaver development life cycle, particularly in leaves. Moreover, this dataset will be a valuable resource to derive hypotheses to mitigate an array of Papaver developmental and secondary metabolite biosynthesis issues in the future.

scholarly journals Staphylococcus aureuscoagulases are exploitable yet stable public goods in clinically relevant conditions

2018 ◽  
Vol 115 (50) ◽  
pp. E11771-E11779 ◽  
Author(s):  
Urvish Trivedi ◽  
Jonas S. Madsen ◽  
Jake Everett ◽  
Cody Fell ◽  
Jakob Russel ◽  
...  
Keyword(s):  
Public Goods ◽  
Social Evolution ◽  
Defense Mechanism ◽  
Critical Role ◽  
Local Population ◽  
Coagulation Cascade ◽  
The Public ◽  
Innate Defense ◽  
The Commons

Coagulation is an innate defense mechanism intended to limit blood loss and trap invading pathogens during infection. However,Staphylococcus aureushas the ability to hijack the coagulation cascade and generate clots via secretion of coagulases. Although manyS. aureushave this characteristic, some do not. The population dynamics regarding this defining trait have yet to be explored. We report here that coagulases are public goods that confer protection against antimicrobials and immune factors within a local population or community, thus promoting growth and virulence. By utilizing variants of a methicillin-resistantS. aureuswe infer that the secretion of coagulases is a cooperative trait, which is subject to exploitation by invading mutants that do not produce the public goods themselves. However, overexploitation, “tragedy of the commons,” does not occur at clinically relevant conditions. Our micrographs indicate this is due to spatial segregation and population viscosity. These findings emphasize the critical role of coagulases in a social evolution context and provide a possible explanation as to why the secretion of these public goods is maintained in mixedS. aureuscommunities.

Hermann Joseph Muller, 1890-1967

1968 ◽  
Vol 14 ◽  
pp. 348-389 ◽  
Keyword(s):  
Molecular Biology ◽  
Human Evolution ◽  
Nobel Prize ◽  
Public Mind ◽  
The Public ◽  
Publication Number ◽  
The Future ◽  
Ionizing Radiations ◽  
Mutagenic Effects ◽  
Heart Condition

Hermann Joseph Muller died on 5 April 1967, at the age of 76, after several years of struggle with a heart condition. Biology has lost one of its outstanding pioneers and leaders. His decisive contributions—both in theory and in experiments, many of them in advance of his time—opened and marked step by step the trail from the Mendelism of the 1910’s to the molecular biology of the 1960’s. His last two papers—prepared in 1965 and 1966—‘The gene material as the initiator and the organizing basis of life’ (369) * and ‘What genetic course will man steer?’ (372)—give a grand view of that trail, of where it has led and of which biological issues the knowledge so acquired presents to mankind. In the public mind Muller’s eminence is based on his vast and profound contributions to experimental genetics, his discovery of the mutagenic effects of ionizing radiations—which motivated the award of the Nobel Prize in 1946—and his efforts to make the genetic hazards of radiations understood and to limit these hazards. There is a widespread tendency to dismiss his concern for the future course of human evolution, and in particular his practical proposals for voluntary germinal choice, as senile deviations, amusing if they were not fraught with danger. Two facts show how wrong is this belief. * Numbers in parentheses refer to publication number in list of published works. Sentences in inverted commas without numbers are from two autobiographical manuscripts of 1936 and 1941, respectively.

scholarly journals Comparison of false-discovery rates of various decoy databases

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Sangjeong Lee ◽  
Heejin Park ◽  
Hyunwoo Kim
Keyword(s):  
Human Protein ◽  
Protein Database ◽  
False Discovery Rates ◽  
Decoy Database ◽  
Protein Databases ◽  
False Discovery ◽  
Large Databases ◽  
Human Protein Database ◽  
Target Database ◽  
Discovery Rates

Abstract Background The target-decoy strategy effectively estimates the false-discovery rate (FDR) by creating a decoy database with a size identical to that of the target database. Decoy databases are created by various methods, such as, the reverse, pseudo-reverse, shuffle, pseudo-shuffle, and the de Bruijn methods. FDR is sometimes over- or under-estimated depending on which decoy database is used because the ratios of redundant peptides in the target databases are different, that is, the numbers of unique (non-redundancy) peptides in the target and decoy databases differ. Results We used two protein databases (the UniProt Saccharomyces cerevisiae protein database and the UniProt human protein database) to compare the FDRs of various decoy databases. When the ratio of redundant peptides in the target database is low, the FDR is not overestimated by any decoy construction method. However, if the ratio of redundant peptides in the target database is high, the FDR is overestimated when the (pseudo) shuffle decoy database is used. Additionally, human and S. cerevisiae six frame translation databases, which are large databases, also showed outcomes similar to that from the UniProt human protein database. Conclusion The FDR must be estimated using the correction factor proposed by Elias and Gygi or that by Kim et al. when (pseudo) shuffle decoy databases are used.

scholarly journals Salt Stress-Responsive Protein Interaction in Hordeum vulgare

2019 ◽  
Vol 17 (3) ◽  
pp. 285-292
Author(s):  
Rajeswari SOMASUNDARAM ◽  
Somasundaram ARUMUGAM ◽  
Neeru SOOD
Keyword(s):  
Salt Stress ◽  
Hordeum Vulgare ◽  
Large Data ◽  
Crop Productivity ◽  
Leaf Sheath ◽  
Theory Analysis ◽  
Protein Database ◽  
Salt Stress Response ◽  
The Public ◽  
Graph Theory Analysis

Salt stress affects crop productivity by altering the biology of the plant and limiting productivity. Hordeum vulgare is the most tolerant cereal crop, with rich genetic resources. The underlying molecular mechanism involved in salt stress response is yet to be comprehensively addressed. A total of 305 proteins are involved in the network. We attempted to find relationships between a few representative stress-responsive proteins of osmotic (pip1), ionic (K+/Na+ ratio in the leaf sheath, HvHAK, HAK4, NHX1 and Ha1), and oxidative stress (APX, CAT1, SOD1) from the public protein database to identify the most influential protein in the network. Further, the salt response proteins were analyzed for their enriched protein domains, Kyoto Encyclopedia of Genes and Genomes pathways, molecular functions, and cell localization. The graph theory analysis of the large data could provide clues for the identification of potential biomarkers for salt stress in barley. An experiment was performed in three accessions of H. vulgare to identify the reliability of the theoretical network relationship in biological systems. The expression of the above-mentioned proteins was further experimentally proven based on the expression and assay.

scholarly journals Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation

2021 ◽  
Vol 12 ◽  
Author(s):  
Basharat Bhat ◽  
Nazir A. Ganai ◽  
Ashutosh Singh ◽  
Rakeeb Mir ◽  
Syed Mudasir Ahmad ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complex Traits ◽  
Defense Mechanism ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Illumina Hiseq ◽  
Single Nucleotide ◽  
The Public ◽  
Assembly Analysis ◽  
Insight Into

Pashmina goats produce the world's finest and the most costly animal fiber (Pashmina) with an average fineness of 11–13 microns and have more evolved mechanisms than any known goat breed around the globe. Despite the repute of Pashmina goat for producing the finest and most sought-after animal fiber, meager information is available in the public domain about Pashmina genomics and transcriptomics. Here we present a 2.94 GB genome sequence from a male Changthangi white Pashmina goat. We generated 294.8 GB (>100X coverage) of the whole-genome sequence using the Illumina HiSeq 2500 sequencer. All cleaned reads were mapped to the goat reference genome (2,922,813,246 bp) which covers 97.84% of the genome. The Unaligned reads were used for de novo assembly resulting in a total of 882 MB non-reference contigs. De novo assembly analysis presented in this study provides important insight into the adaptation of Pashmina goats to cold stress and helps enhance our understanding of this complex phenomenon. A comparison of the Pashmina goat genome with a wild goat genome revealed a total of 2,823 high impact single nucleotide variations and small insertions and deletions, which may be associated with the evolution of Pashmina goats. The Pashmina goat genome sequence provided in this study may improve our understanding of complex traits found in Pashmina goats, such as annual fiber cycling, defense mechanism against hypoxic, survival secret in extremely cold conditions, and adaptation to a sparse diet. In addition, the genes identified from de novo assembly could be utilized in differentiating Pashmina fiber from other fibers to avoid falsification at marketing practices.

scholarly journals Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes

2019 ◽  
Author(s):  
Michelle L. Treiber ◽  
Diana H. Taft ◽  
Ian Korf ◽  
David A. Mills ◽  
Danielle G. Lemay
Keyword(s):  
Target Genes ◽  
Research Question ◽  
Sequencing Depth ◽  
Read Length ◽  
Illumina Platform ◽  
Protein Database ◽  
Library Size ◽  
Specific Target ◽  
Size Selection ◽  
Antimicrobial Resistance Gene

AbstractBackgroundShotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, short reads need to be mapped directly to a gene or protein database. The ability to detect genes in short read sequences is dependent on pre- and post-sequencing decisions. The objective of the current study was to determine how library size selection, read length and format, protein database, e-value threshold, and sequencing depth impact gene-centric analysis of human fecal microbiomes when using DIAMOND, an alignment tool that is up to 20,000 times faster than BLASTX.ResultsUsing metagenomes simulated from a database of experimentally verified protein sequences, we find that read length, e-value threshold, and the choice of protein database dramatically impact detection of a known target, with best performance achieved with longer reads, stricter e-value thresholds, and a custom database. Using publicly available metagenomes, we evaluated library size selection, paired end read strategy, and sequencing depth. Longer read lengths were acheivable by merging paired ends when the sequencing library was size-selected to enable overlaps. When paired ends could not be merged, a congruent strategy in which both ends are independently mapped was acceptable. Sequencing depths of 5 million merged reads minimized the error of abundance estimates of specific target genes, including an antimicrobial resistance gene.ConclusionsShotgun metagenomes of DNA extracted from human fecal samples sequenced using the Illumina platform should be size-selected to enable merging of paired end reads and should be sequenced in the PE150 format with a minimum sequencing depth of 5 million merge-able reads to enable detection of specific target genes. Expecting the merged reads to be 180-250bp in length, the appropriate e-value threshold for DIAMOND would then need to be more strict than the default. Accurate and interpretable results for specific hypotheses will be best obtained using small databases customized for the research question.

scholarly journals Seasonal Variation in Transcriptomic Profiling of Tetrastigma hemsleyanum Fully Developed Tuberous Roots Enriches Candidate Genes in Essential Metabolic Pathways and Phytohormone Signaling

2021 ◽  
Vol 12 ◽  
Author(s):  
Qianqian Xiang ◽  
Siyuan Hu ◽  
Ayalew Ligaba-Osena ◽  
Jiayao Yang ◽  
Fudan Tong ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
High Performance ◽  
Southern China ◽  
Colorimetric Method ◽  
Auxin Signaling ◽  
Endemic Plant ◽  
Protein Database ◽  
Tetrastigma Hemsleyanum ◽  
Transcriptomic Profiling ◽  
Tuberous Roots

Tetrastigma hemsleyanum Diels et Gilg (Sanyeqing, SYQ) is a perennial climbing liana and an endemic plant to southern China. Its tuberous roots (TRs) are used in traditional Chinese medicine for treating some diseases such as high fever, pneumonia, asthma, hepatitis, and cancers. However, the mechanisms underlying the development of TR and the content of flavonoids and phenylpropanoids (FPs) are not well-understood. In this study, we performed a transcriptomic analysis of 12 fully developed TR (FD-TR) samples harvested in four seasons [spring (Sp), summer (Su), autumn (Au), and winter (Wi)] using the RNA-Sequencing (RNA-Seq). We obtained a total of 78.54 Gb raw data and 65,578 unigenes. Then, the unigenes were annotated by using six databases such as non-redundant protein database (NR), Pfam, eggNOG, SWISSProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene ontology (GO). The transcriptomic profiling showed closer relationships between the samples obtained in Su and Au than those obtained in Sp and Wi based on the results of both total unigenes and differentially expressed genes (DEGs). Three pathways, including the biosynthesis of FPs, metabolism of starch and sucrose, and signaling of phytohormones, were highly enriched, suggesting a gene-level seasonal variation. Based on the numbers of DEGs, brassinosteroid (BR) signal transduction factors appeared to play a key role in modulating the development of TRs while most of the auxin signaling genes were mainly activated in Wi and Sp FD-TRs. Most genes in the biosynthesis and biodegradation of starch and biodegradation of cellulose were activated in Wi FD-TRs. As determined by the high performance liquid chromatography (HPLC) and aluminum nitrate colorimetric method, the contents of total flavonoids and most detected FP components increased from Sp to Au but decreased in Wi. Enhanced expression levels of some genes in the biosynthetic pathways of FPs were detected in Su and Au samples, which corroborated well with metabolite content. Our findings provide the first transcriptomic and biochemical data on a seasonal variation in the composition of medically important metabolites in SYQ FD-TRs.

Sign in / Sign up

Export Citation Format

Share Document